1G9Z

LAGLIDADG HOMING ENDONUCLEASE I-CREI / DNA PRODUCT COMPLEX WITH MAGNESIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites.

Chevalier, B.S.Monnat Jr., R.J.Stoddard, B.L.

(2001) Nat.Struct.Mol.Biol. 8: 312-316

  • DOI: 10.1038/86181
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Homing endonucleases, like restriction enzymes, cleave double-stranded DNA at specific target sites. The cleavage mechanism(s) utilized by LAGLIDADG endonucleases have been difficult to elucidate; their active sites are divergent, and only one low re ...

    Homing endonucleases, like restriction enzymes, cleave double-stranded DNA at specific target sites. The cleavage mechanism(s) utilized by LAGLIDADG endonucleases have been difficult to elucidate; their active sites are divergent, and only one low resolution cocrystal structure has been determined. Here we report two high resolution structures of the dimeric I-CreI homing endonuclease bound to DNA: a substrate complex with calcium and a product complex with magnesium. The bound metals in both complexes are verified by manganese anomalous difference maps. The active sites are positioned close together to facilitate cleavage across the DNA minor groove; each contains one metal ion bound between a conserved aspartate (Asp 20) and a single scissile phosphate. A third metal ion bridges the two active sites. This divalent cation is bound between aspartate residues from the active site of each subunit and is in simultaneous contact with the scissile phosphates of both DNA strands. A metal-bound water molecule acts as the nucleophile and is part of an extensive network of ordered water molecules that are positioned by enzyme side chains. These structures illustrate a unique variant of a two-metal endonuclease mechanism is employed by the highly divergent LAGLIDADG enzyme family.


    Organizational Affiliation

    Fred Hutchinson Cancer Research Center, University of Washington, 1100 Fairview Ave. N. A3-023, Seattle, Washington 98109, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA ENDONUCLEASE I-CREI
A, B
152Chlamydomonas reinhardtiiMutation(s): 0 
EC: 3.1.-.-
Find proteins for P05725 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P05725
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*AP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*A)-3'C14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*GP*AP*CP*AP*GP*TP*TP*TP*CP*G)-3'D10N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*AP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*C)-3'E14N/A
Entity ID: 4
MoleculeChainsLengthOrganism
5'-D(P*GP*AP*CP*GP*TP*TP*TP*TP*GP*C)-3'F10N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.000α = 90.00
b = 67.900β = 91.60
c = 88.300γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance